[2023-06-26 23:45:08,972] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:45:08,975] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:45:08,976] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference
[2023-06-26 23:45:10,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:45:10,345] [INFO] Task started: Prodigal
[2023-06-26 23:45:10,345] [INFO] Running command: gunzip -c /var/lib/cwl/stg07bc9613-98f1-47d9-8ae2-2e9703802183/GCA_026708965.1_ASM2670896v1_genomic.fna.gz | prodigal -d GCA_026708965.1_ASM2670896v1_genomic.fna/cds.fna -a GCA_026708965.1_ASM2670896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:45:17,838] [INFO] Task succeeded: Prodigal
[2023-06-26 23:45:17,839] [INFO] Task started: HMMsearch
[2023-06-26 23:45:17,840] [INFO] Running command: hmmsearch --tblout GCA_026708965.1_ASM2670896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/reference_markers.hmm GCA_026708965.1_ASM2670896v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:45:18,090] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:45:18,093] [INFO] Found 6/6 markers.
[2023-06-26 23:45:18,135] [INFO] Query marker FASTA was written to GCA_026708965.1_ASM2670896v1_genomic.fna/markers.fasta
[2023-06-26 23:45:18,136] [INFO] Task started: Blastn
[2023-06-26 23:45:18,136] [INFO] Running command: blastn -query GCA_026708965.1_ASM2670896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/reference_markers.fasta -out GCA_026708965.1_ASM2670896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:45:18,896] [INFO] Task succeeded: Blastn
[2023-06-26 23:45:18,901] [INFO] Selected 30 target genomes.
[2023-06-26 23:45:18,901] [INFO] Target genome list was writen to GCA_026708965.1_ASM2670896v1_genomic.fna/target_genomes.txt
[2023-06-26 23:45:18,963] [INFO] Task started: fastANI
[2023-06-26 23:45:18,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg07bc9613-98f1-47d9-8ae2-2e9703802183/GCA_026708965.1_ASM2670896v1_genomic.fna.gz --refList GCA_026708965.1_ASM2670896v1_genomic.fna/target_genomes.txt --output GCA_026708965.1_ASM2670896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:45:37,271] [INFO] Task succeeded: fastANI
[2023-06-26 23:45:37,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:45:37,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:45:37,287] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:45:37,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:45:37,287] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.3608	55	800	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	76.1288	56	800	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	76.0946	64	800	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	76.0562	63	800	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.9512	64	800	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.6906	53	800	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	75.4747	63	800	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	75.3705	53	800	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	75.3297	94	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:45:37,289] [INFO] DFAST Taxonomy check result was written to GCA_026708965.1_ASM2670896v1_genomic.fna/tc_result.tsv
[2023-06-26 23:45:37,290] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:45:37,290] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:45:37,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/checkm_data
[2023-06-26 23:45:37,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:45:37,326] [INFO] Task started: CheckM
[2023-06-26 23:45:37,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708965.1_ASM2670896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708965.1_ASM2670896v1_genomic.fna/checkm_input GCA_026708965.1_ASM2670896v1_genomic.fna/checkm_result
[2023-06-26 23:46:03,674] [INFO] Task succeeded: CheckM
[2023-06-26 23:46:03,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:46:04,483] [INFO] ===== Completeness check finished =====
[2023-06-26 23:46:04,483] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:46:04,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708965.1_ASM2670896v1_genomic.fna/markers.fasta)
[2023-06-26 23:46:04,484] [INFO] Task started: Blastn
[2023-06-26 23:46:04,484] [INFO] Running command: blastn -query GCA_026708965.1_ASM2670896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc799e4e-94ca-4cf8-b963-cc0d922996d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708965.1_ASM2670896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:46:05,799] [INFO] Task succeeded: Blastn
[2023-06-26 23:46:05,804] [INFO] Selected 17 target genomes.
[2023-06-26 23:46:05,805] [INFO] Target genome list was writen to GCA_026708965.1_ASM2670896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:46:05,820] [INFO] Task started: fastANI
[2023-06-26 23:46:05,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg07bc9613-98f1-47d9-8ae2-2e9703802183/GCA_026708965.1_ASM2670896v1_genomic.fna.gz --refList GCA_026708965.1_ASM2670896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708965.1_ASM2670896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:46:15,437] [INFO] Task succeeded: fastANI
[2023-06-26 23:46:15,451] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:46:15,452] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_007571315.1	s__RKRP01 sp007571315	81.4117	424	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523505.1	s__RKRP01 sp011523505	80.633	431	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009844425.1	s__RKRP01 sp009844425	80.5606	442	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	99.98	99.98	0.98	0.98	3	-
GCA_009838035.1	s__RKRP01 sp009838035	80.5226	408	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	98.62	97.30	0.94	0.92	3	-
GCA_009845905.1	s__RKRP01 sp009845905	80.3088	435	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	99.99	99.98	0.99	0.99	3	-
GCA_014359565.1	s__Immundisolibacter sp014359565	76.4457	61	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	76.3627	57	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_011089885.1	s__XN24 sp011089885	76.3271	69	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355525.1	s__Lysobacter enzymogenes_C	75.8294	82	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442805.1	s__Lysobacter gummosus	75.8133	67	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:46:15,454] [INFO] GTDB search result was written to GCA_026708965.1_ASM2670896v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:46:15,455] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:46:15,458] [INFO] DFAST_QC result json was written to GCA_026708965.1_ASM2670896v1_genomic.fna/dqc_result.json
[2023-06-26 23:46:15,458] [INFO] DFAST_QC completed!
[2023-06-26 23:46:15,458] [INFO] Total running time: 0h1m6s